Landscape and Range Expansion Simulation
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Documentation for package ‘MetaLandSim’ version 2.0.0
Help Pages
| MetaLandSim-package | Landscape And Range Expansion Simulation |
| accept.calculate | Calculate acceptance rates in MCMC chains |
| addpoints | Add a given number of patches to a landscape |
| cabrera | Modified patch occupancy data of Cabrera vole |
| calcmode | Function for mode estimation of a continuous variable |
| cluster.graph | Delivers the number of patches per cluster |
| cluster.id | Classify patches in clusters |
| coda.create | Create files for use with R-package coda. |
| combine.chains | Combines two chains into a single chain. |
| components.graph | Number of components of a landscape |
| convert.graph | Convert data frame to landscape |
| create.parameter.df | Create parameter data frame |
| edge.graph | Produce an edge (links) data frame |
| expansion | Class 'expansion' |
| extract.graph | Extract landscape from span.graph generated list |
| ifm.missing.MCMC | Estimate the 'missing' design incidence function model |
| ifm.naive.MCMC | Estimate the naive design incidence function model |
| ifm.robust.MCMC | Estimate the robust design incidence function model |
| import.shape | Import a shapefile |
| iterate.graph | Simulate landscape series occupation |
| landscape | Class 'landscape' |
| landscape_change | Landscape loosing 5% of patches per time step |
| list.stats | Returning information on a dynamic landscape list |
| manage_expansion_sim | Simulate range expansion simulation |
| manage_landscape_sim | Batch landscape simulation |
| matrix.graph | Returning a matrix with information on connections between patches |
| mc_df | Modified patch occupancy data of Cabrera vole as a data frame |
| merge_order | Internal functions for the MetaLandSim package. |
| MetaLandSim | Landscape And Range Expansion Simulation |
| metapopulation | Class 'metapopulation' |
| metrics.graph | Computes landscape connectivity metrics |
| min_distance | Computes topological distance |
| occ.landscape | Sample landscape with one simulated occupancy snapshot |
| occ.landscape2 | Sample landscape with 10 simulated occupancy snapshots |
| param1 | Sample parameter data frame number 1 |
| param2 | Sample parameter data frame number 2 |
| parameter.estimate | Estimate parameters |
| plotL.graph | Plot one landscape of the list created by span.graph |
| plot_expansion | Graphical display of the expansion simulations |
| plot_graph | Graphical display of the landscape |
| range_expansion | Computes a range expansion model |
| range_raster | Probability of occupancy, dispersal model |
| remove.species | Remove the species occupancy from the landscape |
| removepoints | Remove a given number of patches from the landscape |
| rg_exp | List with range.expansion output |
| rland | Random landscape |
| rland.graph | Creates random landscape graph |
| sim.area | Vector of the areas for each site; here, 100 sites |
| sim.det.20 | Array corresponding to nsites x nyears x nvisits |
| sim.distance | Distance matrix between sampling sites (nsite x nsite). |
| simulatedifm | Set of simulated data to use with the IFM parameter estimation functions. The data were generated using the code provided in "details". |
| simulate_graph | Simulate species occupancy in one dynamic landscape |
| span.graph | Simulate landscape dynamics over a number of time steps |
| species.graph | Simulate landscape occupation |
| spom | Stochastic Patch Occupancy Model |
| summary_landscape | Summarize 'landscape' class objects |
| summary_metapopulation | Summarize 'metapopulation' class objects |
| z.sim | Occupancy data generated with perfect detection. |
| z.sim.20 | Occupancy data generated with perfect detection with approximately 20% of data missing at random. |
| z.sim.20.fa | Occupancy data containing false absences |